@include "rna/_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_BASIC_REPORTS(
    matrices_h5             = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_all_genes_filtered_feature_barcode_matrix.h5",
    filtered_barcodes       = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_barcodes.csv",
    per_barcode_metrics     = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_per_barcode_metrics.csv",
    matrix_computer_summary = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_summary.json",
    barcode_summary         = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ucc6a7a7c4d/files/barcode_summary.h5",
    recovered_cells         = null,
    reference_path          = "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
    summary_jsons           = [
        "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_summary.json",
        "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/_SAMPLE_CELLS_REPORTER/SUBSAMPLE_READS/fork_dimitri-multi/join-ucc6a7a7d79/files/summary.json",
        "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS/fork0/chnk0-ucc6a7a7cde/files/dimitri-multi_summary.json",
        "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/summary.json",
        null,
        null,
        null,
    ],
    cell_bcs_only           = true,
)
